Controlled vocabulary for /pseudogene qualifier

A new qualifier was introduced in version 10.1 (May 2012) of the Feature table definitions: /pseudogene. This qualifier is used to annotate pseudogenes only.

The text below outlines the format and the present list of allowed controlled vocabulary.

Qualifier: /pseudogene=

Definition: indicates that this feature is a pseudogene of the element named by the feature key

Value format: "TYPE"

where TYPE is one of the following: processed, unprocessed, unitary, allelic, unknown

Examples:

/pseudogene="processed"

/pseudogene="unprocessed"

/pseudogene="unitary"

/pseudogene="allelic"

/pseudogene="unknown"

Comment: TYPE is a term taken from the INSDC controlled vocabulary for pseudogenes:

processed: the pseudogene has arisen by reverse transcription of a mRNA into cDNA, followed by reintegration into the genome. Therefore, it has lost any intron/exon structure, and it might have a pseudo-polyA-tail.

unprocessed: the pseudogene has arisen from a copy of the parent gene by duplication followed by accumulation of random mutation. The changes, compared to their functional homolog, include insertions, deletions, premature stop codons, frameshifts and a higher proportion of non-synonymous versus synonymous substitutions.

unitary: the pseudogene has no parent. It is the original gene, which is functional in some species but disrupted in some way (indels, mutation, recombination) in another species or strain.

allelic: a (unitary) pseudogene that is stable in the population but importantly it has a functional alternative allele also in the population. i.e., one strain may have the gene, another strain may have the pseudogene. MHC haplotypes have allelic pseudogenes.

unknown: the submitter does not know the method of pseudogenisation.